Structure of PDB 8dq8 Chain A Binding Site BS02

Receptor Information
>8dq8 Chain A (length=432) Species: 1042876 (Pseudomonas putida S16) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GFDYDVVVVGGGFAGATAARECGLQGYRTLLLEARSRLGGRTFTSRFAGQ
EIELGGTWVHWLQPHVWAEMQRYGLGVVEDPLTNLDKTLIMYNDGIVESI
SPDEFGKNIRIAFEKLCHDAWEVFPRPHEPMFTERARELDKSSVLDRIKT
LGLSRLQQAQINSYMALYAGETTDKFGLPGVLKLFACGGWNYDAFMDTET
HYRIQGGTIGLINAMLTDSGAEVRMSVPVTAVEQVNGGVKIKTDDDEIIT
AGVVVMTVPLNTYKHIDFTPALSKGKQRFIKEGQLSKGAKLYVHVKQNLG
RVFAFADEQQPLNWVQTRDYSDELGTILSITIARKETIDVNDRDAVTREV
QKMFPGVEVLGTAAYDWTADPFSLGAWAAYGVGQLSRLKDLQAAEGRIVF
AGAETSNGWHASIDGAVESGLRAGREVKQLLS
Ligand information
Ligand IDFDA
InChIInChI=1S/C27H35N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,32,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H2,33,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
InChIKeyYPZRHBJKEMOYQH-UYBVJOGSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=C(N2)C(=O)NC(=O)N3)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
CACTVS 3.341Cc1cc2NC3=C(NC(=O)NC3=O)N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
CACTVS 3.341Cc1cc2NC3=C(NC(=O)NC3=O)N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
ACDLabs 10.04O=C3C=2Nc1cc(c(cc1N(C=2NC(=O)N3)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=C(N2)C(=O)NC(=O)N3)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
FormulaC27 H35 N9 O15 P2
NameDIHYDROFLAVINE-ADENINE DINUCLEOTIDE
ChEMBL
DrugBank
ZINCZINC000095099885
PDB chain8dq8 Chain A Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8dq8 Directed evolution unlocks oxygen reactivity for a nicotine degrading flavoenzyme
Resolution1.9 Å
Binding residue
(original residue number in PDB)		V59 G60 G62 A64 E83 A84 R85 G90 R91 G105 G106 T107 W108 V279 V308 P309 W417 F422 A426 W427 G452 A453 S462 I463 A466
Binding residue
(residue number reindexed from 1)		V9 G10 G12 A14 E33 A34 R35 G40 R41 G55 G56 T57 W58 V229 V258 P259 W367 F372 A376 W377 G402 A403 S412 I413 A416
Annotation score1
Enzymatic activity
Enzyme Commision number 1.4.2.2: nicotine dehydrogenase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0016491 oxidoreductase activity
Biological Process
GO:0009820 alkaloid metabolic process
GO:0019608 nicotine catabolic process
Cellular Component
GO:0042597 periplasmic space

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8dq8, PDBe:8dq8, PDBj:8dq8
PDBsum8dq8
PubMed37770699
UniProtF8G0P2|NICA2_PSEP6 Nicotine dehydrogenase (Gene Name=nicA2)

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